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2024

I2PC Seminar Series 2024

Instruct Image Processing Center 2024 Seminar Series Banner

The Instruct i2PC from Instruct Spain is organizing the fifth edition of a seminar series on cryoEM and cryoET methods for image processing. We will be gathering expert developers and users so new and existing methods can gain visibility and users can understand the applications and mechanisms of the presented algorithms.

The webinars will be held online without registration, and they are free. You can join the session and launch questions to the speakers through next link:
https://conectaha.csic.es/b/bla-rkh-dqa-rpn

The contents and speakers will be:

3rd October (10:00 CET Madrid) – Szu-Chi Chung, Department of Applied Mathematics, National Sun Yat-sen University, No. 70, Lienhai Rd, Kaohsiung, Taiwan – Cryo-forum: A processing framework for orientation information recovery with uncertainty measure and its application in cryo-EM image analysis.

2nd December (11:00 CET Madrid) – Andreas Engel, Case Western Reserver University, Switzerland – Robotic grid preparation of vitrified biomolecules from nano litre volumes.

16th December (15:00 CET Madrid) – Joey Davis, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA – Learning structural heterogeneity from cryo-electron sub-tomograms with tomoDRGN.

More speakers and talks are still to be determined for this seminar series. Please stay tuned for more information.

See you there!

Scipion for facilities: Practical Course and Workshop. November 5th – 7th, 2024

Dates: November 5-7th 2024 (3 EU afternoons or 3 east US mornings)

Venue: Hybrid format

Aim: The aim of this meeting is to gather feedback and showcase how facilities are using Scipion, demonstrating its capabilities and benefits for Cryo-EM facilities. The event will feature talks and ample time for discussion, aiming to share experiences with Scipion, discuss operational methodologies, and highlight new developments that can enhance our community’s daily workflow.

Conditions: The workshop will be held at the Spanish National Centre for Biotechnology in Madrid, Spain. For the practical session on November 5, in-person attendance is required, and you must select this option on the registration page to ensure we prepare a machine for you. The main workshop on November 6-7 can be attended either in person or remotely.
No programming skills are required. We will use in-house bigbluebutton conference system. Verify your browser works at https://demo.bigbluebutton.org/

 

Program:

We start at:
San Francisco – 05:00 // Minneapolis – 07:00 // New York – 08:00 // São Paulo – 09:00 // Madrid – 14:00 // London – 13:00
Beijing – 20:00 // Tokyo – 21:00 // Sydney – 23:00

PRACTICAL COURSE

Tuesday 5th November – In person
14:00 – 14:30     Course Overview – Pablo Conesa, Biocomputing Unit CNB – Madrid, Spain.
14:30 – 15:30     On-the-fly processing – Daniel Marchan, Biocomputing Unit CNB – Madrid, Spain.
15:30 – 16:00     Coffee break
16:00 – 17:00     Processing workflows and templates – Daniel Marchan, Biocomputing Unit CNB – Madrid, Spain.
17:00 – 17:45     Scipion with queue systems – Daniel Marchan, Biocomputing Unit CNB – Madrid, Spain.
17:45 – 18:30     Build your own workflow – Support from CNB staff

 

WORKSHOP

Wednesday 6th November – Hybrid
14:00 (CET)      Welcome – Jose María Carazo , Biocomputing Unit CNB – Madrid, Spain.
14:15 – 14:45     An Overview of Scipion in Facilities – Pablo Conesa, Biocomputing Unit CNB – Madrid, Spain.
14:45 – 15:15     Automated on-the-fly data processing in EMhub is fantastic, but what’s next? – Jose Miguel de la Rosa Trevin, St Jude Children’s Research Hospital – Memphis, USA.
15:15 – 15:45     Lab Management with CEITEC: LIMS Demo and Key Features – Radek Veverka, Central European Institute of Technology at Masaryk University – Brno, Czech Republic.
15:45 – 16:15     Coffee break
16:15 – 16:45     Smart Data Collection with Smartscope – Jonathan Bouvette, Princeton University – New Jersey, USA.
16:45 – 17:15     Enhancing Smart Acquisition: Integrating SPA Processing Feedback with the Scipion-EM-SmartScope Plugin – Alberto Garcia, Biocomputing Unit CNB – Madrid, Spain.
17:15 – 18:00     Discussion and user input gathering
 
Thursday 7th November – Hybrid

14.00 (CET)      Enhancing Efficiency: Best Practices and Automations for On-the-Fly Processing in SPA Workflows – Daniel Marchan, Biocomputing Unit CNB – Madrid, Spain.
14:30 – 15:00     NextPyP: A scalable platform for single-particle cryo-EM/ET image analysis – Alberto Bartesaghi Duke University – Durham , USA.
15:00 – 15:30    Using Scipion to enable diverse cryo-ET workflows to explore Neurodegeneration at UCSF – Eric Tse, Institute for Neurodegenerative Diseases UCSF – San Francisco, USA.
15:30 – 16:00     Coffee break
16:00 – 16:30     Scipion use Case: Stream processing at CNB Facility –  Javier Chichon, CryoEM Facility CNB – Madrid, Spain.
16:30 – 17:00     Expanding access to cryo-EM through specimen preparation robotics and platform-independent remote imaging – Mario Borgnia, National Institute of Environmental Health Sciences – Durham, USA
17:00 – 18:00     Discussion and conclusions

National Center for Biotechnology (CNB), Madrid, Spain
Madrid, November 5 – 7, 2024
How to find us: Contact Us – I2PC – Instruct Image Processing Center

REGISTRATION

Registration will be free for all attendees.
Fill your application here

Further details, such as class locations, meeting links, title updates, and instructions for reaching the centre, will be provided in the months leading up to the workshop.

Instruct course on flexibility analysis and integrative modelling using Scipion. Madrid, June 17 – 21, 2024

Venue

Madrid’s Institute for Material Sciences (ICMM-CSIC), Madrid, Spain
Madrid, June 17 – 21, 2024
How to find us: Contact | ICMM (csic.es)

Overall aims and course outline

Cryo-Electron Microscopy has established itself as a mature technique to determine the three-dimensional structure of biological macromolecules. It is currently reaching atomic resolution and is capable of accessing the structure of conformationally heterogeneous samples, as well as macromolecular complexes. It is complementary to other structural techniques like X-ray crystallography and Nuclear Magnetic Resonance and at the moment it is the most rapidly growing technique in atomic structure depositions at public databases like the PDB.
The aim of the course is to introduce attendees to two techniques that are normally needed at the end of the Cryo-Electron Microscopy image processing pipeline: 1) understanding the possible continuous heterogeneity/flexibility of the sample, helping to obtain dynamical information in the form of conformational landscapes, and 2) interpreting the reconstructed map by means of an atomic model. The I2PC has a long tradition of organizing courses of image processing and atomic modelling, with Instruct courses that have been heavily oversubscribed and had to be repeated twice in the same year to be able to attend its demand.
We will use our software platform Scipion to present these two topics. Scipion is an integrative platform that allows interoperability among different software packages. In the domain of flexibility analysis, we include our own developments in Xmipp as well as tools coming from CryoDrgn, ProDy and HEMNMA. For the atomic modelling part, we include software like Coot, Chimera, Refmac, Phenix, and AlphaFold. In addition to simplifying the access to all these software packages in an integrated manner, Scipion adds a traceability and reproducibility layer so that any other researcher can understand the modelling workflow followed to reach a particular model.
This course is addressed to investigators at all levels.

Motivation for the I2PC course on conformational and compositional heterogeneity:
We want this course to help researchers to get introduced in the area of flexibility/heterogeneity analysis, one of the most advanced topics in SPA. For some of the most used methods in the field (some developed by us, some by others) we will
present the theory behind the method and perform a short practical. We will do so within the integrative Scipion Flexibility Hub environment, to help in the use of these multiple methods.

Expected impact for young researchers

Atomic modelling of the CryoEM map is currently at the moment the natural next step once the map is reconstructed. Flexibility analysis is currently not so common, but the advantage of CryoEM is that it can capture the different conformations of the macromolecules under study. Both techniques are valuable assets in young researchers already with a background on image processing in CryoEM.

Contacts

Lead contact:
Carlos Oscar Sorzano
email. coss@cnb.csic.es

Administrative Contact:
Blanca Benitez
email: blanca@cnb.csic.es

Tutors

Marta Martinez (MM) – Modelling specialist @BCU/i2PC
Roberto Marabini (RM) – Professor @UAM, Collaborator @BCU/i2PC
Carlos P. Mata (CM) – Single Particle Analysis specialist @BCU/i2pc
Marcos Gragera(MG) – Single Particle Analysis specialist @BCU/i2pc
David Herreros (DH) – Flexibility Hub head developer @BCU
James Krieger (JK) – Flexibility Analysis specialist @ BCU/i2PC
Carlos-Oscar Sorzano (COS) – Group leader @ BCU, Technical Director @ i2PC

Registration Fee

  • Academic Registration Fee Instruct countries: Predocs & Postdosc 50€
  • Academic Registration Fee Instruct countries: Others 100€
  • Academic Registration Fee Non Instruct countries: Predocs & Postdosc 100€
  • Academic Registration Fee Non Instruct countries: Others 150€
  • Industrial Registration Fee 300€

You can fill your registration here (closed)

Agenda

 Times are expressed in CET time Zone

DAY 1: Modeling

09:00-09:15 Welcome
09:15 – 10:15: Introduction to the compute environment to be used in this course (aws/scipion)
10:15 – 11:00:General introduction to model building in cryo-EM
11:00 – 11:30: Coffee break
11:30 – 13:00: Introduction to the data used in the practical session in homology modeling (details here) and de novo modeling
13:00-13:30: Map preprocessing I
13:30-14:30: Lunch break
14:30-16:00: Getting a first estimate of the model “de novo” (AlphaFold & ModelAngelo) and by sequence homology. 
16:00-16:30: Coffee break
16:30-17:00: Continuation of first estimation
17:00-17:30: Structure analysis: Structure comparison
17:30-18:00: Rigid Fitting of Initial Models
18:00: End of the day

DAY 2: Modelling

09:00-09:30: Review yesterday’s work 
09:30-11:00: Flexible fitting (Coot) and Validation
11:00-11:30: Coffee break
11:30-13:30: Flexible fitting and Validation
13:30-14:30: Lunch break
14:30-15:00: Review Kahoot students, teacher
15:00-16:00: Coffee break
16:30-17:00 Building the model of the whole protein
Chain merge & symmetrization
17:00-17:30: Submission of structures to EMDB. Understanding the validation report. Haemoglobin PDB full validation report 
Comparison validation scores PDB structure
17:30: Structure analysis: chain contacts Structural search
18:30:End of the day

DAY 3: Flexibility

9:30 – 10:00: Introduction to macromolecular flexibility and Flexibility Hub
10:00 – 10:15: Presentation of the dataset and workflows of the day (Zernike3D – HetSIREN)
10:15 – 11:00: Zernike3Deep (Theory)
11:00 – 11:30: Coffee break
11:30 – 12:30: Zernike3Deep (Practice)
12:30 – 13:00: HetSIREN (Theory)
13:00 – 14:00: Lunch break
14:00 – 15:00: HetSIREN (Practice)
15:00 – 15:30: Dimensionality reduction of estimated landscapes
15:30 – 16:00: Landscape exploration: interactive tools
16:00 – 16:30: Coffee break
16:00 – 17:00: Landscape exploration: interactive tools
17:00 – 17:30: End of the day

DAY 4: Flexibility

9:30 – 10:00: Review from the previous day
10:00 – 10:15: Presentation of the workflows of the day (FlexConsensus – ZART – CryoDRGN)
10:15 – 11:00: Should we trust our conformational landscapes? FlexConsensus (Theory)
11:00 – 11:30: Should we trust our conformational landscapes? FlexConsensus (Practice)
11:30 – 12:00: Coffee break
12:00 – 12:30: Should we trust our conformational landscapes? FlexConsensus (Practice)
12:30 – 13:00: Beyond motion blurr: ZART and flexible refinement (Theory)
13:00 – 14:00: Lunch break
14:00 – 15:00: Beyond motion blurr: ZART and flexible refinement (Practice)
15:00 – 15:30: CryoDRGN (Theory)
15:30 – 16:00: CryoDRGN (Practice)
16:00 – 16:30: Coffee break
16:30 – 17:00: CryoDRGN (Practice)
17:00 – 17:30: Landscape exploration: interactive tools
17:30 – 18:00: End of the day

DAY 5: Flexibility

9:30 – 9:45: Review from the previous day
9:45 – 10:00: Presentation of the workflows of the day (ContinuousFlex – 3DVA – 3DFlex – Prody)
10:00 – 11:00: ContinuousFlex
11:00 – 11:30: Coffee break
11:30 – 12:00: 3DVA (Theory)
12:00 – 13:00: 3DVA (Practice)
13:00 – 14:00: Lunch break
14:00 – 14:30: 3DFlex (Theory)
14:30 – 15:30: 3DFlex (Practice)
15:30 – 16:00: Prody
16:00 – 16:30: Coffee break
16:00 – 17:00: Prody
17:00 – 17:30: End of the day (closing remarks)

I2PC Course on Single Particle Analysis by CryoEM. Madrid, 20 – 22 March, 2024

Venue

National Center for Biotechnology (CNB), Madrid, Spain
Madrid, March 20 – 22, 2024
How to find us: https://idospece.i2pc.margaro.eus/contact-us/

Overall aims and course outline

Cryo-Electron Microscopy has established as a mature technique to determine the three-dimensional structure of biological macromolecules. It is currently reaching atomic resolution and it is capable of accessing to the structure of conformationally heterogeneous samples, as well as macromolecular complexes. It is complementary to other structural techniques like X-ray crystallography and Nuclear Magnetic Resonance and at the moment it is the most rapidly growing technique in atomic structure depositions at public databases like PDB.

The aim of the course is to give an overall overview of the image processing in single particle analysis (SPA). The I2PC has a long tradition of organizing courses of image processing and atomic modelling, with Instruct courses that have been heavily oversubscribed and had to be repeated twice in the same year to be able to attend its demand.

With the experience gained in the organization of virtual and in-person courses, we plan to organize this course in an in-person modality. 20 people will be able to physically attend.

The course is aimed at researchers of all levels wanting to adopt electron microscopy as one of the tools at their disposal for elucidating biological structures.

Expected impact for young researchers

CryoEM is the most rapidly growing structural technique. PhD students as well as young post-docs will certainly benefit from approaching this technique. Knowing it will open new doors to new positions worldwide.

Tutors: I2PC: Carlos Oscar Sorzano Sánchez, Jose-María Carazo, Marcos Gragera, Carlos Perez Mata
CryoEM CNB-CSIC: Francisco Javier Chichón.
Contacts: Lead contact:  Carlos Oscar Sorzano
E-mail: coss@cnb.csic.es
Administrative Contact: Blanca Benitez
E-mail: blanca@cnb.csic.es

 

 

 

 

 

Agenda

 Times are expressed in CET time Zone

DAY 1: 9:30 Morning session:
– Movie alignment, Screening micrographs and CTF
– Particle picking and screening

13:00 Lunch Break

14:00 Afternoon session:
– Particle picking and screening
– 2D classification

17:00 End of day
DAY 2: 9:30 Morning session:
– Initial volume
– 3D classification

13:00 Lunch Break

14:00 Afternoon session:
– 3D classification advanced (masking, classification with no alignment…)
– 3D reconstruction

17:00 End of day
DAY 3: 9:30 Morning session:
– Sharpening, local resolution and validation

13:00 Lunch Break

14:00 Afternoon session:
– One-to-one troubleshooting meeting

17:00 End of day

Registration Fee

ACOMMODATIONS

REGISTRATION

The online registration will be open until  February 16th.
Fill your application here (closed). 

I2PC – Instruct-RI Hubs hybrid course on Electron Tomography and Subtomogram Averaging. Madrid, December 10 – 13, 2024

VENUE

Hybrid course.
December 10 – 13, 2024 from 16:00 to 21:30 CET.
You do not need to install any special software to connect. A modern browser should be enough.

 

Overall aims and course outline

By using image processing algorithms, it becomes possible to pinpoint the macromolecules of interest within the electron tomograms. Subsequently, researchers can extract small subtomograms from these locations and identify similar particles, facilitating their averaging and the recognition of diverse conformations. This process, referred to as subtomogram averaging, has played a pivotal role in elucidating an increasing number of macromolecular structures, achieving resolutions ranging from 20 to 3 A.

The course is designed to offer a comprehensive overview of the whole image processing workflow in Electron Tomography (ET). This includes tasks such as aligning the tilt series, reconstructing 3D tomograms, identifying particles, performing subtomogram averaging or even to perform a tomogram segmentation, all inside Scipion integration framework.  

With the experience gained in the organisation of virtual and in-person courses, we intend to organise this course in a hybrid format. We will be able to accommodate up to 20 individuals for in-person attendance. However, other 20 participants will attend remotely. In total, we can host 40 attendees. 

The course is aimed at researchers of all levels wanting to adopt electron microscopy as one of the tools at their disposal for elucidating biological structures

Expected impact for young researchers

CryoET is one of the most promising structural techniques, and it bridges the gap between structural and molecular biology and cell biology. Ph.D. students, as well as post-docs, will undoubtedly benefit from approaching this technique. Knowing it will open new doors to new positions worldwide.

Prerequisites

  • You will need to bring a laptop with a modern browser
  • We will provide machines with the required software through Amazon Web Services.
  • We will provide coffee breaks

Tutors: I2PC: Carlos Oscar Sorzano Sánchez, Jose-María Carazo, Pablo Conesa, Jorge Jiménez & Jose Luis Vilas.
CryoEM CNB-CSIC: Francisco Javier Chichón.
Contacts: Lead contact:  Carlos Oscar Sorzano
E-mail: coss@cnb.csic.es
Administrative Contact: Blanca Benitez & Oscar Saiz
E-mail: blanca@cnb.csic.es; oscar.saiz@cnb.csic.es

Agenda

 Times are expressed in CET time Zone

DAY 1: 

From movies to tomograms

15:00 – Welcome – (José Maria Carazo & Carlos Oscar Sorzano)
15:15 – Introduction to Electron Tomography – (José Luis Vilas)
15:35 – Course Introduction (Machines & Scipion) – (Pablo Conesa)
16:00 – Import Tilt Series, Automatic alignment – (José Luis Vilas)
17:00 – 15 minutes break
17:15 – CTF estimation and correction – (José Luis Vilas)
18:30 – Tomogram reconstruction – (José Luis Vilas)
20:00 – eTomo – (José Luis Vilas)
20:30 – End of session

DAY 2: 

From tomograms to subtomograms: Picking

15:00 – ThermoFisher – Cryo-FIB microscopes for cryo-electron tomography and volume electron microscopy
16:00- Non-directional picking with cryolo and SPA leap – (Pablo Conesa)
17:00- 15 minutes break
17:15 – Dynamo – (Pablo Conesa)
20:30 – End of session

DAY 3: 

Processing subtomograms

 15:00 – Classic Subtomogram averaging – (Jorge Jiménez)
16:00 – Subtomogram averaging with RELION5 (I) – (Jorge Jiménez)
17:00- 15 minutes break
19:00 – Subtomogram averaging  – (Jorge Jiménez)
20:30 – End of session

DAY 4: 

Tomogram interpretation

15:00 – Tomogram segmentation: SuRVos– (Javier Chichón)
20:30 – End of course. Wrap up

 

Registration Fee

ACOMMODATIONS

REGISTRATION

Fill your application here (closed). 

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